The New Threat
by Joker's Apprentince
Summary: On a investigation of a newe planet Athena Shepard, Daughter of famous human Jason Shepard, discovers a strange new people. But with a new threat looming over the horizon she will need the help of their #1 Hyperactive Knucklehead Ninja. Rated M for safety
1. Chapter 1

So at this point I have no idea what i'm gonna do to help further my story, The End War.

Probably just delete the the thing and have done with it.

Besides it's not living up to the expectations I had for it.

Though if I get rid of the naruto characters and just make it a regular Mass Effect fanfic I could make a prequel to this new one sort.

-is puzzling over it-

Oh well that's up to you fine readers.

-sees a lawyer-

I DO NOT OWN NARUTO OR MASS EFFECT

-does a Biotic Slam on the lawyer-

Now on with the show

Chapter 1: The war comes to an end...

Ashley Williams, Lieutenant Commander of the Systems Alliance and most recently a Spectre, the galaxy's elite soldiers hand picked from all the council races, however all these accomplishments paled in comparison to the little pink bundle she currently held in arms. Smiling down at the baby she noticed black tufts of hair sticking out of the little girls head. It was then the little girl yawned and seemed to snuggle closer to her. Smiling a smile that only a mother holding her baby for the first time could manage Ashley leaned forward a little and kissed her daughter's forehead.

"Welcome to the galaxy Athena Gracelyn Shepard," Ashley said lovingly to the little bundle of joy in her arms, who seemed to smile and give a babyish giggle at her new name. Meanwhile in a small, relatively unexplored area of the galaxy a small blonde headed boy cried out for the parents who would never hold him, never love him, and would never be there to comfort him from the hated glares of the people who were supposed to revere him as a hero.

20 years later...

Lieutenant Commander Athena Gracelyn Shepard was impatiently drumming her fingers against her Vindicator Assault Rifle, which she modded with a precision scope and a stability dampener for better aim. Sighing as she sat aboard the Kodiak Drop Shuttle she, once again, began to wonder what made this new planet so damn important. She then gave up when her omni-tool blinked with a message from her mother, Spectre Ashley Williams. Once again she ran over what made her different from her mother, her mother was a straight running and gunning soldier, Athena Shepard was a Vanguard, a mixture of a biotic and a soldier, where the biotics came from she had no idea seeing how her dad, Jason Shepard was a Infiltrator, a mixture of tech and soldiering, her mother liked Ulysses, Athena preferred Edgar Allen Poe, her mother always held a day of remembrance for her long dead father, Athena didn't see any reason in mourning a man she never knew, and lastly her mother was calm in a firefight while Athena just shot the place up and called it a day. Her mom also didn't like it when she hung out with her Aunt Jack, her fears were somewhat well founded seeing how Athena had gotten her first, and so far only tattoo, on a rare visit to Earth, it was a tribal fox ready to slam it's paw down on a black blob located on her right shoulder. Answering the call she saw a miniature version of her mom hovering about an half a centimeter above her omni-tool. Her mom's dark auburn hair was starting to show streaks of gray, you could almost clearly see the wrinkles on her face, her chocolate colored eyes that still sparkled with warmth, even though she was like forty something.

"Hey Gracy," her mom greeted her with a smile and a warm voice, using her childhood pet name.

"Hey mom," she said, rolling her eyes slightly. Causing her mom's smile to widen a little, looking up from the projection a little she saw quite a few of her male comrades pointing at her mother's projection and making what appeared to be lewd comments. Glaring at them she looked back down at her mom and tried her best not to use a biotic slam, a trick her Aunt Miranda had taught her, on all of them.

"So what's new Gracy," her mom asked, smiling at her more than likely well aware of the comments made by her male counterparts.

"We're investigating a planet on the very edge of the Outer rim," Athena explained, knowing her mom would find out either from her Spectre channels or when the official report crossed some officers desk.

"oh why's that," her mom asked, the smile never leaving her face.

"I don't know just following orders right now," Athena answered, it was then a red light went off signaling they were about to land, "gotta go mom."

With that she cut the transmission then looked up at all the males in the shuttle.

"Any of you dipshits even try to make an advance on my mom and I will beat you so bad they'll need a mop to pick you up off the floor," Athena threatened, causing all the males to gulp knowing she meant of word of the threat she just issued. It was then the side hatch to the shuttle opened and everyone climbed out to a vast and seemingly endless forest, weapons at the ready they began moving in a northern direction and after about two hours of walking they were met by a very tall stone wall. Splitting into two teams one team followed the wall to the left and the other followed it right. Athena's team had followed to the left and were met by a giant gate with two guys in green flak jackets, blue long sleeve shirts and dark blue capri looking pants and they wore a a weird bandana with a metal plate with what looked like a leaf etched into set center on their foreheads. Making sure the two stayed asleep, by hitting them lightly on the temple with their gun butts. Walking into the city they saw a bunch of civilians walking milling about and shop owners hocking there wares in a strange language, looking at their omni-tool's built in translators it was translating with a little effort, apparently the people were speaking in a dialect similar to Japanese. Grinning at this Athena turned to the rest of the group, and was surprised to find she was the highest ranking person there at the time.

"OK people split up and explore, anything unusual or that might prove an asset to the Alliance or the Council races report it back to me," she ordered her troops, with a quick nod they split up and took off in various directions. Deciding now would be as good a time as any to try and blend in to the current environment she found a abandoned building and began undoing the clasps of her armor, leaving her in a t-shirt, semi-skin tight pants, and black boots. Sighing she walked out to try and mingle with the locals.

Naruto's POV...

Naruto had just woken up and went about his morning ritual, brushing his teeth, making a cup of ramen, showering, making a cup of ramen, and getting dressed. When he walked outside he smiled and began to wonder what awesome jutsu he was gonna learn today. At the age of 20 Naruto had seen and done more then most other ninja twice his age, seeing as how he was the unofficial new Gama Sennin, but they only knocked him up to the rank of Chunin. Now it wasn't because of clan politics, seeing how he was good terms with the Clan heads and future clan heads, nor was it the councils, for the Hokage had final say in who got promoted, no the reason he hadn't gone past chunin was because he didn't truly want the rank of Jonin, though it was a massive stepping stone for his rise to Kage. He couldn't explain why he just didn't want it. Sighing he looked in a plate glass window at his reflection, his blonde hair still stuck up at odd angles, his blue eyes and long since lost that spark of mischief they once had, three whisker marks on each cheek, marking him as the Jinchuriki of Kurama, the Nine-tailed Fox, he was currently wearing a black long sleeve shirt, he long traded the orange for dark blues and blacks, as his new ANBU style shinobi pants had proven, black shinobi sandals, a black Konoha headband, and he was wearing a orange coat with black flames along the hems, the coat going to mid thigh. Sighing he decided to hit up his old sensei Kakashi Hatake to see if he had any new training regimes he could try out or new jutsu he could learn, when he was immediately stopped in his tracks by the most beautiful female he had ever seen, and he had seen a lot of beautiful women, she stood at roughly 5'10" with a athletic build, wavy black hair that stopped at her shoulders, dark blue eyes that seemed curious of everything, a somewhat sharply angled face, and her deeply tan skin tone gave her a somewhat exotic look, but the clothes she was wearing were odd, she wore what looked like a short sleeve ANBU top, semi-skin tight Jonin style pants, and dark looking shoes that couldn't possibly be shinobi sandals. Following the girl he noticed she seemed to be heading no where in particular, just looking around, because she was headed into what the more privileged citizens of Konoha called the Blackwater slums, the "bad part" of Konoha. The Blackwater Slums weren't necessarily that bad, sure it had a gang or two, but as long as you knew one the bosses you were fine, and this girl probably didn't no anyone.

Needless to say the minute she entered the slums she was swarmed by one of the gangs, the Kageryu of Naruto was correct. Sighing Naruto walked up and decided to make his presence known by unleashing a ungodly amount of Killer Intent. Looking past the girl all the gang members paled considerable.

"Naruto-sama," one of the gang members announced, bowing low with his forehead almost touching the ground. Sighing Naruto walked over to the bowing gang member and bopped him on the head.

"Kenji how many times do I have to tell you never to refer to me as Naruto-sama," Naruto asked with a sigh, causing Kenji to get a thoughtful look on his face.

"If I had to guess I'd say now makes it 279 times Naruto-sama," Kenji announced, before turning back to the girl.

"She's with me Kenji," Naruto announced quickly, causing Kenji to nod and back off. Naruto immediately grabbed the girls wrist and lead her around a corner.

"What the fuck possessed you to come here," Naruto asked with a hard glint in his eyes, the strange girl just waved him off.

"I could have taken care of them," the girl said, not the least bit worried about the situation she could've been in. Sighing Naruto was about to argue with her until he heard a beeping, looking around for what might have caused the beeping Naruto turned back to look at the girl, only to notice that she was staring down at a weird orange gauntlet that had a circle over the back of the hand and circular segments that went around the forearm up to the elbow. It was then a picture appeared of a human with his hair cut close to his scalp, light blue eyes, and a scar going from just below his earlobe to the right corner of his mouth.

"We found something you're gonna want to see," the male said in a thick kind of drawl. It was then the image of the man faded to show Kakashi flashing through a set of hand signs just before a dragon of water emerged from a nearby pond and surged toward a group of people in strange armor that seemed to cover their whole bodies, and just when the Water dragon slammed into the people they had a faint purple aura surround them just before they were swept away. The girl looked awestruck at Kakashi's jutsu, while Naruto was curious as to what that faint aura was, and the odd objects they were holding were.

"The Commander Athena Shepard," the girl, now identified as Athena, announced, "copy that continue mission and report in."

Naruto looked even more confused, just before the girl collapsed, falling right into Naruto's arms, right as a ANBU in a hawk mask appeared.

"Ah thank you Naruto-san we've been tailing her and her friends since they entered the village," the ANBU said, "now if you will allow me to take her to Ibiki."

Naruto merely shook his head and wind shunshined to the leaf village's I&T division.

Meanwhile in a unknown corner of the galaxy...

A figure sat dragging on a cigar imported from Earth, a small island country call Cuba was who manufactured the cigar. He was looking over a datapad when a female figure, wrapped in a dark black trench coat walked in.

"Ah Ms. Leng glad you could join me," the figure in the chair said as a female with straight black hair that went to her mid back, a black visor covered her eyes, a black shirt with a elongated hexagon with two bent rectangles on the sides. The figure said calmly tapping the ashes of his cigar into a built in ashtray on his chair.

"We have a situation that needs your particular skill set," the figure in the chair stated, taking a long drag on his cigar, "it appears one Athena Gracelyn Shepard as discovered a new planet with the inhabitants possessing peculiar abilities."

With that he played the footage from one of his agents that had been apart of the team sent to investigate the planet. The footage showed two people fighting at speeds that were surprisingly quick, then it changed over to a pink haired woman bent over a patient on the ground, and her hands were emitting a bright green glow as the massive gash on the patients chest knit itself shut, and the last bit of footage showed a man with silver hair moving his hands at blinding speed just before the water in the pond next to him rose up and formed into a dragon slamming into the agent and decimating his shields in mere seconds. Blinking behind her visor Kasumi Leng was at the least a little impressed at this planet's inhabitants.

"Your mission is to convince some this planet's inhabitants to join our cause," the man in the chair stated simply. Kasumi nodded and then walked out of the room. As soon as she left the room the figure tapped a button on his chair and a photo of Athena Gracelyn Shepard, the figure sneered at the photo, ready to put his lit cigar to it but stopped himself.

"Soon dear sister," The figure said menacingly, putting out his cigar as he grabbed a glass and poured it almost to the brim with vodka. Then he set to planning on how he was going to take his vengeance on his sister, and bring glory to his father's name by doing what he couldn't, controlling the Reapers and using them to combat a evil far greater than then Jason Shepard could comprehend, a evil for the time being, called simply the Reavers.

OK ik Reavers, Reapers wow big whoop, but bear with me.

Also if you haven't noticed this fic is set 20 yrs after Mass Effect 3 then you need to get checked.

Also if you haven't noticed there will be alcohol and tobacco references.

Also there will be romance options available for Athena, one of which if you haven't guessed is Naruto, or I can do an entirely different set of romance options for Naruto.

However I will put a poll on my profile up to see if you people want me to make the End War a prequel to this or not, if so I will go back and write Naruto and Hinata out of it.

Well just be sure to leave me plenty reviews, favs, and alerts.

Till the next post.

This is Dark Soldier signing out.

-screen goes black just after showing two swords crossed over a the chest of a skeletal soldier-


	2. Alliance Marines meet Konoha Shinobi

So mostly positive reviews for The New Threat.

Hopefully it goes the way I want it to.

Also the romance options for Naruto so far are: Athena Shepard.

Romance option for Athena Shepard so far: Naruto Uzumaki-Namikaze.

More romance options will be added as the story goes on, though at chapter 6 I should have all the romance options up.

-spots a lawyer-

Alright I do not own Naruto or Mass Effect

-uses a biotic charge to knock the lawyer off screen-

Now on with the show

Chapter 2: Alliance Marines meet Konoha Shinobi...

Athena was starting to come to see a dark, abyssal looking room, and when she tried to move her hands to rub some of the tiredness from her eyes she realized they wouldn't move. Getting a frightened look on her face she turned her head around and caught a glimpse of thick chains and pieces of paper over them. It was then she heard a door open, turning her head quickly, she saw a man in his late forties with a bandana with a strip of metal in the middle with a leaf etched into it, a dark blue trench coat, dark blue pants, a dark blue shirt, and dark blue sandals and standing next to him was a woman in her late thirties to early forties dress in a tan trench coat with her hair done up in a pineapple fashion, purple eyes that had a mischievous glint to them, a somewhat revealing black shirt that stopped at her midriff with a fish net shirt on over it.

"My name is Ibiki Morino," the man stated, " and this is Anko Mitarashi, and we'll be your interrogators today."

Gulping Athena thought of all the horrible things they might do, when the blonde boy from before walked in.

"Ibiki I'll handle this one," the boy stated, all the man known as Ibiki did was nod and walk out of the room with the lady known as Anko. The boy calmly grabbed a chair from the opposite wall and turn it backwards before sitting in it. The boy just stared at her for a few minutes before walking behind her and undoing her chains, causing them and the paper to fall to the floor. Shocked she didn't know the boy had spoke until he repeated the question.

"What brought to Konoha," the boy asked patiently.

"To be honest we just came to your planet for any kind of valuable resources," Athena answered, not even sure what made her answer. Nodding the blonde just sat there a little longer, then his eyes kind of widened as if he just saw a ghost from his past. Reaching his hand forward he wrapped his hand around a chain that was on her neck, just before he yanked it off and looked at it. In the light she saw a cross engraved with the word Diligo, engraved into it.

"Where did you get this," the boy demanded, practically shoving the cross in her face.

"It belonged to my father," Athena answered, somewhat confused by the boys reaction. It was then she saw the boy dig around in one of the pouches attached to his leg and pull out a identical cross, exact same material and everything. The boy just sighed and went back to sitting in his chair before he handed her cross back, and extended his hand.

"Name's Naruto," the boy, identified as Naruto stated simply. Athena looked at his hand then extended her own, firmly shaking Naruto's hand.

"Athena Shepard," Athena stated simply, causing Naruto to quirk his eyebrow.

"You got a very peculiar name," Naruto stated, causing Athena to sigh with closed eyes.

"Blame my mom and dad," Athena stated, "Dad's side of the family had a thing for naming their kids after important figures of Greek mythology."

Shrugging Naruto sat there and then they just talked for what seemed like hours, about everything and nothing, and making sure not give away anything classified. Looking down at his watch, which he just remembered having, his eyes nearly bugged out.

"It's been fun but I gotta run," Naruto said hurriedly as he bolted out the door and ran for all he was worth. When he finally stopped running he was standing in front of the door to the Suna embassy, and walked inside. But as he got closer to he heard his girlfriend giggling, cracking his girlfriend's door open, and hoping for the best, he saw his girlfriend Temari no Subaku having sex with Shikamaru Nara, someone Naruto consider to practically be his brother. Turning around Naruto calmly left the embassy and didn't look back. The next day everyone noticed the change in Naruto's demeanor, he was more serious and avoided the Suna Embassy at all cost, which was odd considering he always tried to be near the place to check on Temari. It was promptly one o'clock in the afternoon when he reported into the Interrogation and Torture division of the Konoha Shinobi Force. When he walked into Athena's cell he was shocked to see her doing push ups with her feet on the chair. Curiously he watched her for a few seconds, before he went and tried to join her.

"If you want me to move all you gotta do is ask," Athena stated, moving her feet over so Naruto could move his onto the chair.

"First to twenty wins," Naruto asked, with a fox like grin on his face. Athena's only response was a smirk and she began doing push ups. Smirking Naruto enhanced his muscles with chakra and began moving faster than Athena had ever thought possible, needless to say he hit 20 pushups in no time at all.

"OK how did you do that," Athena asked, completely perplexed by what happened. Naruto just looked at her like he would a child that asked a dumb question.

"Don't they have chakra where you're from," Naruto asked incredulously, the response he got from Athena was anything but knowing.

"OK let me explain," Naruto stated simply, as he pulled a chalkboard diagram, of a human body with the kanji for physical and spiritual on two halves of a circle at the center of the body, from seemingly out of nowhere, as he began to explain, "Chakra is the combination of both physical and spiritual energy. Chakra has a variety of uses in the world of Shinobi, such as being used to provide a boost to physical capabilities, creating jutsu, or being used to activate certain seals. However certain clans have a Kekkai Genkai, or Bloodline Limit, which grants them either a special kind of chakra, the ability to close chakra pathways, or physical mutations."

When Naruto finished his explanation he pushed the chalkboard diagram out of sight, and it once again vanished. Mystified by this explanation Athena looked down at her hands and back up at Naruto.

"Now do you have anything like that where you're from," Naruto asked, pride evident in his tone and the smirk on his face. Smirking herself Athena used a Singularity on him, causing him to float aimlessly in the air, she then quickly followed up a warp, specifically targeted at Naruto's jacket, and then used a pull, sending him flying across the room, where he went headfirst into the wall and promptly slid down. When he didn't get up, Athena ran over to check on him, thinking she may have hurt him badly. But her fears where unfounded as Naruto jumped up like nothing happened and stood spread eagle with a smile, that the Cheshire Cat would be envious of.

"That was awesome," Naruto shouted, and this time he started asking questions, " What was that? Is that all you can do? How powerful can you make it?"

Not knowing what to do with the sudden bombardment of questions, Athena grabbed her head and was about to use a biotic slam on Naruto to get a few minutes of quiet, when a very old feminine voice interrupted his barrage of questions.

"Naruto give our guest room breathe," ordered the voice. Turning quickly she saw a woman who could be older then 39, with long blonde hair done into two pigtails, boobs that had to be artificial, a gray kimono top, blue high heel like sandals, a green over coat, and dark blue capri looking pants that stopped just above her ankles. Chuckling sheepishly Naruto put a hand behind his head and gave a fox like grin.

"Sure thing Granny," Naruto replied, causing the woman to sigh. It was then someone else walked into the room. He stood 6'0, with light blue eyes, hair shaved close to his head, a scar going from the middle of his forehead to just below his right eye, and dark blue S7 armor with silver stripes.

"Thanks to your friend here we were able to verify your story," the woman stated, "though the council has requested that both of you show up to a meeting we are holding, right now."

Sighing, Athena walked behind and to the right of the lady, were as Naruto walked to the back of the group of four. They walked for about a half hour, which they only knew cause Naruto kept checking his watch, when they stepped into a wide circular room, which was divided into two sections with a boxed in set of seats close to the top of second section. One section had eleven seats filled, the eleventh one Naruto himself filled. The other half was clearly filled with nothing but civilians, seeing as how they all acted snobbish and like they were better than everyone else and that their opinion was the most important. It was at this point the lady Naruto called Granny turned to them.

"alright the section on the left," she stated quietly, pointing to the eleven people, "is the shinobi council, which consists of the Eleven Clan heads, with Naruto of course. Those fools over there," she stated, with obvious venom in her voice, "is the Civilian council."

Nodding in understanding, they sat next to "Granny" and waited.

"Order, Order," "Granny" called, silencing the Civilian council, " OK now that that is settled. This meeting of the Council of Konohagakure no Sato was called on accounts of the strangers having came inside our village, bearing unknown weapons and armor. I trust you have all read the reports I sent out, stating precisely what both these strangers and their comrades have told me."

"They should be executed," shouted a pink haired bansh- I mean woman from the civilian half of the council. Immediately the civilian council roared in approval and began clamoring for the heads of the strangers. It was then they heard a loud crash and turned in the direction of the sound, only to see Naruto with a Rasengan in hand, right over the now destroyed table.

"I have a better idea," Naruto stated as he walked toward the front of the room, "Honorable Councilmen, "insert cough from the females" and Councilwomen I propose that we release them."

This proposal didn't sit well with the Civilian portion of the council who immediately let out cries of outrage, only to be silenced by Naruto forming another Rasengan.

"I also propose that I go with them as a ambassador of good will to show we mean no harm," Naruto proclaimed, getting a nod of approval from the Shinobi council, who didn't want to see a war just four years after they got out of one, "and to learn their motives and so we can potential learn things that will better our flourishing society."

Thinking of the potential profit they could make from such a thing even the Civilian council let out cries of approval.

"All those in favor of sending a ambassador of good will with these strangers when they leave," Tsunade asked, unanimous across the board everyone raised their hands.

"Lady Hokage since it was my idea I volunteer to be the Ambassador for our people," Naruto said calmly, shocking most of the people there.

"Alright Naruto I hereby bestow Sannin Travel Rights on you and give a S class mission of being an Ambassador of Good Will for our village to these people," Tsunade said with a smirk, "this Council meeting is adjourned."

With that Naruto disappeared in a flash of yellow, not to be seen for the rest of the day. When the meeting was adjourned Athena was about to go retrieve her arms and armor, when she felt a hand on her shoulder. Seeing "Granny" give her the universal sign for follow me. Following "Granny" she found herself in a office with a desk piled high with paperwork and a bay window just behind the desk. "Granny" calmly sat down at the desk and interlocked her hands in front of her mouth.

"Can I ask a favor of you," "Granny" asked tiredly, like someone who had lost too many loved ones and someone who had lived too many years in one war or another.

"Sure," Athena replied curiously, wondering what it could be. The answer came when she saw a tear in "Granny"'s eye.

"Please take care of Naruto for me," "Granny" requested sadly, tears beginning to freely flow from her eye. All Athena could do in this situation is nod dumbly, before she walked out of the building, found the building that had her arms and armor, put them on, and left the village hidden in the leaves, to find Naruto walking close behind her, following her to the drop ship that would take them back to the Alliance Carrier _USS Ulysses_. After that they would set off for council space, to report their findings to the Citadel Council.

In a unknown part of space...

A figure sat in a chair, downing his fifth of straight Jack and puffing on a cigar, when a woman who could be described as 21st century model beautiful walked in, looking at a datapad. Looking away from the eight holo screens arrayed before him the figure looked up at the woman, she had the standard Cerberus uniform, she had deep chestnut hair that stopped just past her shoulders, electric blue eyes, and a figure even a Asari would kill to get. But a little known fact about the woman was that she was practically on the "Illusive Man's" speed dial for top class assassination missions and the like.

"Ms. Nyx I have a special mission that requires the particular talents of you and Ms. Leng," the "Illusive Man" stated, causing the woman to stop and smile a sickly sweet smile.

"Who's the target," Nyx asked sweetly, a little too sweetly if you were to ask some people. However her boss merely did a corner smile and tapped the ashes off his cigar.

"You and Ms. Leng are to tail one Athena Shepard and her new associate Naruto Namikaze, find out everything you can about them, likes, dislikes, romance interests, down to the last fling they had, dreams for the future, I want to know everything about them."

Nodding Nyx left and packed for what could be a very long mission, seeing as how her and Kasumi Leng couldn't stand each other. While the "Illusive Man" just sat there and pondered what pawns he should move across the board to further ensure the survival of Humanity, and then push them to the top of the galactic food chain.

"Your move sister make it a good one," "The Illusive Man" stated, looking at all the dossiers on every member of Athena's future crew.

So how did you people like that?

Yes I know having Naruto find out his girlfriend was cheating on him was horrible, but it had to be done.

Also this will not, I repeat this will not, be a Naruhina as much as I like that pairing it ain't happening.

Also how will Naruto react to a galaxy hundreds of years ahead of his own, as far as technology and weapons are concerned.

Also no I will be featuring any of the romance interests from the Mass Effect trilogy, mostly because they are too old in my opinion, or they are just dead for unexplainable reasons.

Also what surprises await Athena when she gets back to council space?

Who will be her new crew?

And what's Naruto's deal with that cross.

Till then this is Dark Soldier signing out.

-screen goes black after showing two rusted, scratched, and chipped broadswords crossed over the chest of a skeletal soldier, with a rusted viking helmet on top it's head-


End file.
